def test_command(command_name, kwargs):
reset()
pdbx_file = pdbx.PDBxFile.read(join(data_dir, "1l2y.cif"))
structure = pdbx.get_structure(pdbx_file)
structure.bonds = struc.connect_via_residue_names(structure)
pymol_obj = PyMOLObject.from_structure(structure)
command = getattr(PyMOLObject, command_name)
command(pymol_obj, **kwargs)
def test_both_directions(path, state):
pdbx_file = pdbx.PDBxFile.read(path)
ref_array = pdbx.get_structure(pdbx_file, model=state)
ref_array.bonds = struc.connect_via_residue_names(ref_array)
reset()
test_array = PyMOLObject.from_structure(ref_array) \
.to_structure(state=state, include_bonds=True)
for cat in ref_array.get_annotation_categories():
assert (test_array.get_annotation(cat) == ref_array.get_annotation(cat)
).all()
assert np.allclose(test_array.coord, ref_array.coord)
assert test_array.bonds == ref_array.bonds
def test_to_biotite(path, altloc, state):
pdbx_file = pdbx.PDBxFile.read(path)
ref_array = pdbx.get_structure(pdbx_file, model=state, altloc=altloc)
reset()
cmd.load(path, "test")
test_array = PyMOLObject("test").to_structure(state=state, altloc=altloc)
for cat in [
c for c in ref_array.get_annotation_categories()
if c != "altloc_id"
]:
assert (test_array.get_annotation(cat) == ref_array.get_annotation(cat)
).all()
assert np.allclose(test_array.coord, ref_array.coord)
def test_to_pymol(path):
reset()
cmd.load(path, "test")
ref_model = cmd.get_model("test", 1)
pdbx_file = pdbx.PDBxFile.read(path)
atom_array = pdbx.get_structure(
pdbx_file, model=1, extra_fields=["b_factor", "occupancy", "charge"])
test_model = convert_to_chempy_model(atom_array)
test_atoms = test_model.atom
ref_atoms = [atom for atom in ref_model.atom if atom.alt in ("", "A")]
assert len(test_atoms) == len(ref_atoms)
for test_atom, ref_atom in zip(test_atoms, ref_atoms):
assert test_atom.symbol == ref_atom.symbol
assert test_atom.name == ref_atom.name
assert test_atom.resn == ref_atom.resn
assert test_atom.ins_code == ref_atom.ins_code
assert test_atom.resi_number == ref_atom.resi_number
assert test_atom.b == pytest.approx(ref_atom.b)
assert test_atom.q == pytest.approx(ref_atom.q)
assert test_atom.hetatm == ref_atom.hetatm
assert test_atom.chain == ref_atom.chain
assert test_atom.coord == pytest.approx(ref_atom.coord)
def test_select(random_seed):
reset()
pdbx_file = pdbx.PDBxFile.read(join(data_dir, "1l2y.cif"))
array = pdbx.get_structure(pdbx_file, model=1)
# Add bonds to avoid warning
array.bonds = struc.connect_via_residue_names(array)
# Use B factor as indicator if the selection was correctly applied
array.set_annotation("b_factor", np.zeros(array.array_length()))
pymol_object = PyMOLObject.from_structure(array)
np.random.seed(random_seed)
ref_mask = np.random.choice([False, True], array.array_length())
# The method that is actually tested
test_selection = pymol_object.where(ref_mask)
# Set B factor of all masked atoms to 1
cmd.alter(test_selection, "b=1.0")
test_b_factor = pymol_object.to_structure(state=1).b_factor
# Get the mask from the occupancy back again
test_mask = (test_b_factor == 1.0)
assert np.array_equal(test_mask, ref_mask)